Correlating overrepresented upstream motifs to gene expression: a computational approach to regulatory element discovery in eukaryotesReportar como inadecuado




Correlating overrepresented upstream motifs to gene expression: a computational approach to regulatory element discovery in eukaryotes - Descarga este documento en PDF. Documentación en PDF para descargar gratis. Disponible también para leer online.

BMC Bioinformatics

, 3:7

First Online: 14 February 2002Received: 13 December 2001Accepted: 14 February 2002

Abstract

BackgroundGene regulation in eukaryotes is mainly effected through transcription factors binding to rather short recognition motifs generally located upstream of the coding region. We present a novel computational method to identify regulatory elements in the upstream region of eukaryotic genes. The genes are grouped in sets sharing an overrepresented short motif in their upstream sequence. For each set, the average expression level from a microarray experiment is determined: If this level is significantly higher or lower than the average taken over the whole genome, then the overerpresented motif shared by the genes in the set is likely to play a role in their regulation.

ResultsThe method was tested by applying it to the genome of Saccharomyces cerevisiae, using the publicly available results of a DNA microarray experiment, in which expression levels for virtually all the genes were measured during the diauxic shift from fermentation to respiration. Several known motifs were correctly identified, and a new candidate regulatory sequence was determined.

ConclusionsWe have described and successfully tested a simple computational method to identify upstream motifs relevant to gene regulation in eukaryotes by studying the statistical correlation between overepresented upstream motifs and gene expression levels.

Electronic supplementary materialThe online version of this article doi:10.1186-1471-2105-3-7 contains supplementary material, which is available to authorized users.

Download fulltext PDF



Autor: Michele Caselle - Ferdinando Di Cunto - Paolo Provero

Fuente: https://link.springer.com/



DESCARGAR PDF




Documentos relacionados